We have a track record of developing and publicly releasing software for physiological image processing and analysis. Our ethos is to try and make the work we do available for other people to try out and use, seeking to be:
Quantiphyse is a GUI viewing and analysis package for biomedical imaging data. As well as generic visualisation and processing functionality, it contains a set of plugins for processing specific kinds of physiological imaging data including ASL, DCE, CEST, DSC and quantitative BOLD.
These are FSL-based pipelines for processing different types of medical imaging data. They utilise Fabber for the model fitting but also include pre and post processing specific to the data type.
oxford_aslbut with some new features and also supporting multiphase and vessel-encoded ASL data.
Fabber is a Bayesian model fitting framework which uses the Variational Bayes algorithm to do fast model fitting of nonlinear forward models. It is a fully Bayesian solution allowing the specification of prior information and the production of posterior distributions. The algorithm can be used on any serial data, but we have also designed it to be suitable for serial imaging data.
SVB is an implementation of Stochastic Variational Bayes for inferring on medical imaging timeseries data. It aims to solve the same problem as Fabber by an alternative means which may provide advantages in some cases.
Toblerone contains tools for surface based analysis including projection and partial volume estimation. Toblerone can estimate partial volumes across the brain using surface segmentations (for example, those from FreeSurfer and FSL FIRST).
Regtricks contains tools for manipulating, combining and applying image transformations. It is not a replacement for image registration tools (eg FSL FLIRT), but it does make working with the output of these tools easier. In particular it enables transformations to be combined within an object oriented interface and applied to data in a single step, avoiding multiple interpolations.
The FSL course contains a practical session on ASL-MRI processing using the Basil/Oxford ASL toolbox.
Neuroimaging Primers is a series of short, accessible
textbooks focused on MRI-based neuroimaging. Under
Example Boxes you can find a set of interactive
tutorials on ASL-MRI data processing using the Basil/Oxford ASL toolbox.
The Variational Bayes Tutorial contains interactive code demonstrating simple implementations of Analytic and Stochastic variational Bayes.
Tutorials for DCE, qBOLD and ASL using Quantiphyse are included in the general Quantiphyse documentation